Either do it from a boot to windows or from windows running in puppy in virtualbox.
As to being able to do it with say wine in puppy by mounting the NTFS windows partition and then running robocopy with that mounted windows partition as target, might work.
But...
I would make a backup of the windows partition just in case of a failure.

I gave up on using thumb drives for this and switched to dropbox (syncs two computers via the web plus online access to your material). works fine on windows and puppy (I'm often bouncing between 3 different computers sometimes on at the same time, and have had no problems)

http://db.tt/YHyqu9pN

above is my referral link (which gives you and me a bit of extra free space). Or if referrals aren't for you, you can google dropbox and go from there.

sfeeley- I've thought about using dropbox ... so far I'm holding back because of how often I'm working w/o an internet connection, so the usb stick still seems attractive. Because I'm only using the web interface, doesn't look like the referral will help you any